In case of human, for example, one of the reasons for difference between individual subjects in susceptibility to diseases, reactivity to medical drugs, susceptibility to side effect and the like may be due to the involvement of a genetic mutation (base polymorphism of gene). And so, focusing attention on this difference of nucleotide sequence, studies on the exploration of a suitable therapy for the individual constitution have been progressing. In addition, the base polymorphism of gene can also be genetic markers for various diseases. Therefore, the clarification of such base polymorphism is important from the clinical point of view, and the establishment of a method for analyzing nucleotide sequence which is capable of detecting the respective mutant gene and a method for identifying such base polymorphism has long been desired.
In addition, in the field of diagnosis of infectious diseases, there is an occasion where the infecting microorganism has developed resistance to drug by a genetic mutation. Therefore, for the purpose of determining whether the microorganism isolated from the patient has developed resistance to the medical agent, the detection of a genetic mutation in the microorganism isolated from the patient is particularly important from a viewpoint of diagnostic methodology and also for the selection of appropriate therapeutic treatment.
For example, it has been clarified that a mutation of rpoB gene coding for RNA polymerase B subunit of genus Mycobacterium is involved in development of resistance to rifampicin in human tubercle bacillus (Mycobacterium tuberculosis), and the mutation in rpoB gene was observed for about 95% of the rifampicin-resistant tubercle bacilli. And so, it may be possible to figure out whether the tubercle bacillus is resistant to rifampicin or not by detecting this gene and by determining the existence or non-existence of genetic mutation.
In addition, as to the mutation in rpoB gene involved in the rifampicin resistance of tubercle bacillus, various patterns have been reported (VIVEK KAPUR, et al., J. Clin. Microbiol. 1944. p. 1095-1098). Therefore, if the detection of plural number of mutant genes can be performed at the same time, improved accuracy in the diagnosis and increased throughput (the amount of information processed in a certain period) can be expected.
As to the tubercle bacillus, the genetic mutation involved in the resistance to other medical drugs has also been studied, and it is now coming to light the patterns for the respective mutations.
Another example showing effectiveness of the detection of mutation is the detection of MRSA. That is, as the methicillin-resistant Streptococcus aureus (MRSA) has mec gene, the resistance to methicillin can be recognized by the detection of the mec gene (MRSA can be detected).
However, in order to detect the existence of mutant gene such as a point mutation, a single nucleotide polymorphism, and the like, difference of only one base in a huge genomic nucleotide sequence has to be detected, and in consequence, a very high specificity is required.
Examples of known analytical technique of the nucleotide sequence which is conventionally and commonly used are, for example, the determination method of nucleotide sequence determination (sequencing method), TaqMan™ probe method (Genome Res., vol. 6, p. 986, 1996), RFLP (restriction fragment length polymorphism) method (J. Clin. Invest., vol. 72, p. 1262, 1983), ASP (allele-specific primer) method (WO 01/42498), ASO (allele-specific oligoprobe) method (Nature, vol. 324, p. 163, 1986), Single base extension method (Proc. Natl. Acad. Sci. USA, vol. 94, p. 10756, 1997), Pyrosequencing method (Analytical Biochemistry, vol. 244, p. 367, 1997), Invader™ method (Nature Biotech., vol. 17, p. 292, 1999), and so on.
Among these methods, the method of nucleotide sequence determination, TaqMan™ probe method, RFLP method, ASO method, Single base extension method, Pyrosequencing method and the like are the methods in which a region comprising a mutation or a polymorphism is amplified in advance using nucleic acid amplification technique such as Polymerase Chain Reaction (PCR), then the detection procedure is performed. Therefore, in order to obtain a clear signal with reduced background, to obtain a specific amplification product is primarily quite important.
Invader™ method is an accepted method in principle, which can detect the mutation and polymorphism without any amplification reaction. However, there are many cases where the sensitivity is insufficient for the detection when the method is practiced without amplification reaction. Practically, same as the case with other methods, it is important to amplify the nucleotide of the measuring object to be detected in advance.
Further, in the ASP method, after amplifying the mutant allele specifically by PCR using a mutant DNA-specific oligonucleotide comprised of about 20 bases and a template DNA, the PCR product obtained is subjected to gel electrophoresis, and the existence of a mutant allele is detected by detecting a band. This method is eventually suitable for testing a large number of samples efficiently.
However, in the conventional methods using PCR as described above including the ASP method, there are some cases where a primer extension product is obtained even when mismatches exist in the primer, and so that there exists difficulty in obtaining a specific amplification product. Therefore, the method is problematic in terms of stringency.
In addition, there is a method which uses a primer having a nucleoside with a base which is not complementary to a target gene at the second position from 3′end, and setting the polymorphic site to be detected at the 3′end thereof, incidentally the method has been modified from the ASP method based on the knowledge that the polymorphism-specific primer having SNP site at the second position from the 3′ end thereof recognizes the polymorphism precisely. There is a publication reporting that, in this method, detection of the polymorphic site existing at the 3′end is improved, in comparison with a primer having a nucleoside with a base complementary to a target gene at the second position from 3′end (Non-patent Document 1). However, even though this method is used, in some cases, such a primer extension product is obtained even when mismatches exist at the 3′end of the primer, and eventually, the method still had a problem in terms of detection sensitivity.
Further, a method using an oligonucleotide as a primer has been reported (Patent Document 1), in which the 3′end of the nucleotide sequence thereof is set in a polymorphic site, and a 2′-O, 4′-C-ethylene nucleotide unit is used as the third nucleotide from 3′end thereof.
In the above-described Patent Document, using a primer complementary to a wild type sequence in which the third nucleotide from 3′end thereof is a 2′-O,4′-C-ethylene nucleotide unit (Example 1 of Patent Document 1) and a primer complementary to a mutant type sequence in which the third nucleotide from 3′ end thereof is a 2′-O,4′-C-ethylene nucleotide unit (Example 2 of Patent Document 1), PCR has been performed using a wild type sample as a template (Test Example 1 of Patent Document 1). In this case, amplification of gene was confirmed when the primer complementary to the wild type DNA sequence was used, and amplification of gene was not confirmed when the primer complementary to the mutant type DNA sequence was used. For this reason, in the above-described reference, it has been stated that the selective amplification of gene can be performed by this method.
However, it cannot be concluded only by the above-described results that the above-described primer, which is complementary to the wild type sequence, is specific for the detection of the wild type. That is, unless the result showing that when PCR with a wild type DNA sample as a template is performed by using a primer complementary to a wild type sequence, the primer extension products can be obtained, however, when PCR with a mutant type DNA sample as a template is performed by using the same primer, the primer extension products can not be obtained, there can not be a proof showing that the above-described primer is capable of detecting wild type specifically.
In fact, even when PCR is performed using “a primer which amplifies mutant type” and a sample from wild type gene according to this method, there is a problem that the primer extension products is obtained (emergence of false positive). Namely, there is a problem that even when the primer extension product could be obtained by performing PCR using this primer for a sample, which sample is unclear whether it is wild type or mutant type, still the sample cannot be determined whether it is wild type.
As to a possible cause of the above-described problem, the following reason can be considered. That is, the thermostable DNA polymerase used for PCR has a 5′→3′ polymerase activity and concurrently has a 3′→5′ exonuclease activity. Therefore, when a primer capable of amplifying the mutant type is bound to a sample comprising the wild type gene, the nucleotide base allocated at the 3′end of the primer, which base is the same or complementary to the mutant nucleotide gene, will be cleaved at the PCR step by the 3′→5′ exonuclease activity of the thermostable DNA polymerase. Therefore, the 3′ end of the above-described primer recognizes completely the gene sequence of the wild type sample, which normally should not be recognized, and the extension reaction according to the primer sequence is started by the action of the DNA polymerase. In consequence, it is considered that, even though a primer which should amplify the mutant type has been used, and PCR has been performed using a sample comprising wild type gene as a template, the primer extension product has been produced, and thus such a nonspecific amplification is occurred.
In addition, in general, the “specificity” is defined as the ability to give a decision for negative as negative. And so, as a method for improving the specificity in the analysis of mutation and polymorphism using a nucleic acid amplification reaction, a method for inhibiting nonspecific amplification (emergence of false positive amplification) can be considered. As a means for this purpose, optimization of amplification condition (increase of anneal temperature, decrease of cycle number, lowering of enzyme amount, change of enzyme species, decrease of dNTP concentration, decrease of Mg concentration, decrease of template DNA concentration, and the like), modification of primer design, utilization of hot start method using antibody or aptamer, utilization of modified oligonucleotide (PNA and LNA, and the like) which have been said to increase the specificity, and the like are considered. However, there are some cases where these methods are effective for the suppression of nonspecific amplification, but in many cases the effectiveness is insufficient and optionally the suppression is also occurred in the specific amplification, and these each has drawback.
From these circumstances, establishment of a method for detecting mutation(s) in nucleotide sequence with exclusion of false positive and with high specificity has been desired.
Patent Document 1: JP-A-2005-323583
Patent Document 2: JP-A-1993-271224
Non-patent Document 1: Bioorganic & Medical Chemistry, 2003, vol. 11, pp. 2211-2226
Non-patent Document 2: VIVEK KAPUR et al., J. Clin. Microbiol., vol. 32, No. 4, 1994, pp. 1095-1098
Non-patent Document3: Koji Morita et al., Bioorganic & Medical Chemistry Letters, vol. 12, 2002, pp. 73-76